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PDBsum entry 2c9o

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
2c9o
Jmol
Contents
Protein chains
398 a.a. *
311 a.a. *
Ligands
ADP ×3
Waters ×158
* Residue conservation analysis
PDB id:
2c9o
Name: Hydrolase
Title: 3d structure of the human ruvb-like helicase ruvbl1
Structure: Ruvb-like 1. Chain: a, b, c. Synonym: ruvbl1,49-kda tata box-binding protein- interacting protein, 49 kda tbp-interacting protein, tip49a, pontin 52,nuclear matrix protein 238,nmp 238,54 kda erythrocyte cytosolic protein, ecp-54, tip60- associated protein 54-alpha, tap54-alpha. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 511693. Expression_system_variant: de3.
Biol. unit: Hexamer (from PDB file)
Resolution:
2.20Å     R-factor:   0.209     R-free:   0.257
Authors: P.M.Matias,S.Gorynia,P.Donner,M.A.Carrondo
Key ref:
P.M.Matias et al. (2006). Crystal structure of the human AAA+ protein RuvBL1. J Biol Chem, 281, 38918-38929. PubMed id: 17060327 DOI: 10.1074/jbc.M605625200
Date:
14-Dec-05     Release date:   23-Oct-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9Y265  (RUVB1_HUMAN) -  RuvB-like 1
Seq:
Struc:
456 a.a.
398 a.a.
Protein chain
Pfam   ArchSchema ?
Q9Y265  (RUVB1_HUMAN) -  RuvB-like 1
Seq:
Struc:
456 a.a.
311 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B, C: E.C.3.6.4.12  - Dna helicase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O = ADP + phosphate
ATP
+ H(2)O
=
ADP
Bound ligand (Het Group name = ADP)
corresponds exactly
+ phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     MLL1 complex   15 terms 
  Biological process     cell cycle   18 terms 
  Biochemical function     nucleotide binding     8 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M605625200 J Biol Chem 281:38918-38929 (2006)
PubMed id: 17060327  
 
 
Crystal structure of the human AAA+ protein RuvBL1.
P.M.Matias, S.Gorynia, P.Donner, M.A.Carrondo.
 
  ABSTRACT  
 
RuvBL1 is an evolutionarily highly conserved eukaryotic protein belonging to the AAA(+)-family of ATPases (ATPase associated with diverse cellular activities). It plays important roles in essential signaling pathways such as the c-Myc and Wnt pathways in chromatin remodeling, transcriptional and developmental regulation, and DNA repair and apoptosis. Herein we present the three-dimensional structure of the selenomethionine variant of human RuvBL1 refined using diffraction data to 2.2A of resolution. The crystal structure of the hexamer is formed of ADP-bound RuvBL1 monomers. The monomers contain three domains, of which the first and the third are involved in ATP binding and hydrolysis. Although it has been shown that ATPase activity of RuvBL1 is needed for several in vivo functions, we could only detect a marginal activity with the purified protein. Structural homology and DNA binding studies demonstrate that the second domain, which is unique among AAA(+) proteins and not present in the bacterial homolog RuvB, is a novel DNA/RNA-binding domain. We were able to demonstrate that RuvBL1 interacted with single-stranded DNA/RNA and double-stranded DNA. The structure of the RuvBL1.ADP complex, combined with our biochemical results, suggest that although RuvBL1 has all the structural characteristics of a molecular motor, even of an ATP-driven helicase, one or more as yet undetermined cofactors are needed for its enzymatic activity.
 
  Selected figure(s)  
 
Figure 2.
FIGURE 2. The DNA binding region in RuvBL1 domain II. A, stereoview of the protein C^ trace (gold) and ssDNA ball-and-stick representation (carbon, nitrogen, oxygen, and phosphorus atoms are colored gray, blue, red, and green, respectively) of the RPA molecule (PDB 1JMC) superimposed onto the DNA binding region of RuvBL1 DII (residues 127-233; cyan). The long loops in the N-terminal domain of RPA that interact with ssDNA (arrows 1 and 3) correspond to a disordered loop and a much shorter loop (arrow 2) in RuvBL1 DII. B, view of the electrostatic potential of the RPA molecule mapped at its molecular surface. The molecular surface was calculated with MSMS (65) using a probe radius of 1.4 Å, and the electrostatic potential was calculated with MEAD (66) using an ionic strength of 0.1 M, dielectric constants of 4.0 and 80.0 for the protein and the exterior, respectively, and a temperature of 300 K. The range of potentials shown spans -5 (red) to +5 kT/e (blue) units. C, view of the electrostatic potential of the DNA binding region of RuvBL1 DII mapped at its molecular surface. The molecular surface and the electrostatic potential were calculated as described above for the whole RuvBL1 hexamer, but for clarity only the DNA binding region of RuvBL1 DII is represented. As a visual aid, the ssDNA molecule bound to RPA is represented in ball-and-stick (Carbon, nitrogen, oxygen, and phosphorus atoms are colored gray, blue, red, and green, respectively). The view in B and C is the same as in Fig. 2A. Drawings were prepared with DINO.
Figure 3.
FIGURE 3. The RuvBL1 hexamer. A, ribbon diagram of the RuvBL1 hexamer (side view). Adjacent monomers are colored light gray and gold. One gold monomer is colored in the same way as in Fig. 1B to highlight its domain structure. The hexamer herein represented is the crystallographic hexamer, formed by monomers A around the crystallographic 6-fold axis. The bound ADP molecules are depicted in space-filling mode, where each atom is represented by a sphere with a diameter twice its conventional van der Waals radius. Carbon, nitrogen, oxygen, and phosphorus atoms are colored gray, blue, red, and green, respectively. B, ribbon diagram of the RuvBL1 hexamer (top view). The coloring scheme is as in A. Drawings were prepared with DINO.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 38918-38929) copyright 2006.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21111787 A.Grigoletto, P.Lestienne, and J.Rosenbaum (2011).
The multifaceted proteins Reptin and Pontin as major players in cancer.
  Biochim Biophys Acta, 1815, 147-157.  
22048315 O.Mueller-Cajar, M.Stotz, P.Wendler, F.U.Hartl, A.Bracher, and M.Hayer-Hartl (2011).
Structure and function of the AAA+ protein CbbX, a red-type Rubisco activase.
  Nature, 479, 194-199.
PDB codes: 3syk 3syl 3zuh
20412048 A.Niewiarowski, A.S.Bradley, J.Gor, A.R.McKay, S.J.Perkins, and I.R.Tsaneva (2010).
Oligomeric assembly and interactions within the human RuvB-like RuvBL1 and RuvBL2 complexes.
  Biochem J, 429, 113-125.  
20553504 C.Papin, O.Humbert, A.Kalashnikova, K.Eckert, S.Morera, E.Käs, and M.Grigoriev (2010).
3'- to 5' DNA unwinding by TIP49b proteins.
  FEBS J, 277, 2705-2714.  
19887446 C.Zhao, E.A.Matveeva, Q.Ren, and S.W.Whiteheart (2010).
Dissecting the N-ethylmaleimide-sensitive factor: required elements of the N and D1 domains.
  J Biol Chem, 285, 761-772.  
20512115 H.Walbott, S.Mouffok, R.Capeyrou, S.Lebaron, O.Humbert, H.van Tilbeurgh, Y.Henry, and N.Leulliot (2010).
Prp43p contains a processive helicase structural architecture with a specific regulatory domain.
  EMBO J, 29, 2194-2204.
PDB code: 2xau
20130677 J.Huen, Y.Kakihara, F.Ugwu, K.L.Cheung, J.Ortega, and W.A.Houry (2010).
Rvb1-Rvb2: essential ATP-dependent helicases for critical complexes.
  Biochem Cell Biol, 88, 29-40.  
20130681 K.L.Cheung, J.Huen, W.A.Houry, and J.Ortega (2010).
Comparison of the multiple oligomeric structures observed for the Rvb1 and Rvb2 proteins.
  Biochem Cell Biol, 88, 77-88.  
20722407 P.Jing, F.Haque, D.Shu, C.Montemagno, and P.Guo (2010).
One-way traffic of a viral motor channel for double-stranded DNA translocation.
  Nano Lett, 10, 3620-3627.  
19217392 B.Bae, Y.H.Chen, A.Costa, S.Onesti, J.S.Brunzelle, Y.Lin, I.K.Cann, and S.K.Nair (2009).
Insights into the architecture of the replicative helicase from the structure of an archaeal MCM homolog.
  Structure, 17, 211-222.
PDB code: 3f8t
19620283 K.S.McKeegan, C.M.Debieux, and N.J.Watkins (2009).
Evidence that the AAA+ proteins TIP48 and TIP49 bridge interactions between 15.5K and the related NOP56 and NOP58 proteins during box C/D snoRNP biogenesis.
  Mol Cell Biol, 29, 4971-4981.  
19946136 M.L.Bochman, and A.Schwacha (2009).
The Mcm complex: unwinding the mechanism of a replicative helicase.
  Microbiol Mol Biol Rev, 73, 652-683.  
19062292 R.C.Conaway, and J.W.Conaway (2009).
The INO80 chromatin remodeling complex in transcription, replication and repair.
  Trends Biochem Sci, 34, 71-77.  
19524533 S.Jha, and A.Dutta (2009).
RVB1/RVB2: running rings around molecular biology.
  Mol Cell, 34, 521-533.  
18358808 A.S.Venteicher, Z.Meng, P.J.Mason, T.D.Veenstra, and S.E.Artandi (2008).
Identification of ATPases pontin and reptin as telomerase components essential for holoenzyme assembly.
  Cell, 132, 945-957.  
18329872 E.J.Enemark, and L.Joshua-Tor (2008).
On helicases and other motor proteins.
  Curr Opin Struct Biol, 18, 243-257.  
18940606 E.Torreira, S.Jha, J.R.López-Blanco, E.Arias-Palomo, P.Chacón, C.Cañas, S.Ayora, A.Dutta, and O.Llorca (2008).
Architecture of the pontin/reptin complex, essential in the assembly of several macromolecular complexes.
  Structure, 16, 1511-1520.  
18466635 J.Snider, G.Thibault, and W.A.Houry (2008).
The AAA+ superfamily of functionally diverse proteins.
  Genome Biol, 9, 216.  
  18765919 S.Gorynia, P.M.Matias, T.M.Bandeiras, P.Donner, and M.A.Carrondo (2008).
Cloning, expression, purification, crystallization and preliminary X-ray analysis of the human RuvBL1-RuvBL2 complex.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 840-846.  
18849995 X.Zhang, and D.B.Wigley (2008).
The 'glutamate switch' provides a link between ATPase activity and ligand binding in AAA+ proteins.
  Nat Struct Mol Biol, 15, 1223-1227.  
17720918 D.L.Updike, and S.E.Mango (2007).
Genetic suppressors of Caenorhabditis elegans pha-4/FoxA identify the predicted AAA helicase ruvb-1/RuvB.
  Genetics, 177, 819-833.  
17761535 G.Giorgio, M.Alfieri, C.Prattichizzo, A.Zullo, S.Cairo, and B.Franco (2007).
Functional characterization of the OFD1 protein reveals a nuclear localization and physical interaction with subunits of a chromatin remodeling Complex.
  Mol Biol Cell, 18, 4397-4404.  
18023171 P.A.Tucker, and L.Sallai (2007).
The AAA+ superfamily--a myriad of motions.
  Curr Opin Struct Biol, 17, 641-652.  
17320397 P.Gallant (2007).
Control of transcription by Pontin and Reptin.
  Trends Cell Biol, 17, 187-192.  
17984971 S.Lall (2007).
Primers on chromatin.
  Nat Struct Mol Biol, 14, 1110-1115.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.